Nonequilibrium entropic bounds for Darwinian replicators

Life evolved on our planet by means of a combination of Darwinian selection and innovations leading to higher levels of complexity. The emergence and selection of replicating entities is a central problem in prebiotic evolution. Theoretical models have shown how populations of different types of replicating entities exclude or coexist with other classes of replicators. Models are typically kinetic, based on standard replicator equations. On the other hand, the presence of thermodynamical constrains for these systems remain an open question. This is largely due to the lack of a general theory of out of statistical methods for systems far from equilibrium. Nonetheless, a first approach to this problem has been put forward in a series of novel developements in non-equilibrium physics, under the rubric of the extended second law of thermodynamics. The work presented here is twofold: firstly, we review this theoretical framework and provide a brief description of the three fundamental replicator types in prebiotic evolution: parabolic, malthusian and hyperbolic. Finally, we employ these previously mentioned techinques to explore how replicators are constrained by thermodynamics.Comment: 12 Pages, 5 Figure

Magnetism, FeS colloids, and Origins of Life

A number of features of living systems: reversible interactions and weak bonds underlying motor-dynamics; gel-sol transitions; cellular connected fractal organization; asymmetry in interactions and organization; quantum coherent phenomena; to name some, can have a natural accounting via $physical$ interactions, which we therefore seek to incorporate by expanding the horizons of `chemistry-only' approaches to the origins of life. It is suggested that the magnetic 'face' of the minerals from the inorganic world, recognized to have played a pivotal role in initiating Life, may throw light on some of these issues. A magnetic environment in the form of rocks in the Hadean Ocean could have enabled the accretion and therefore an ordered confinement of super-paramagnetic colloids within a structured phase. A moderate H-field can help magnetic nano-particles to not only overcome thermal fluctuations but also harness them. Such controlled dynamics brings in the possibility of accessing quantum effects, which together with frustrations in magnetic ordering and hysteresis (a natural mechanism for a primitive memory) could throw light on the birth of biological information which, as Abel argues, requires a combination of order and complexity. This scenario gains strength from observations of scale-free framboidal forms of the greigite mineral, with a magnetic basis of assembly. And greigite's metabolic potential plays a key role in the mound scenario of Russell and coworkers-an expansion of which is suggested for including magnetism.Comment: 42 pages, 5 figures, to be published in A.R. Memorial volume, Ed Krishnaswami Alladi, Springer 201

Exploiting limited valence patchy particles to understand autocatalytic kinetics

Autocatalysis, i.e., the speeding up of a reaction through the very same molecule which is produced, is common in chemistry, biophysics, and material science. Rate-equation-based approaches are often used to model the time dependence of products, but the key physical mechanisms behind the reaction cannot be properly recognized. Here, we develop a patchy particle model inspired by a bicomponent reactive mixture and endowed with adjustable autocatalytic ability. Such a coarse-grained model captures all general features of an autocatalytic aggregation process that takes place under controlled and realistic conditions, including crowded environments. Simulation reveals that a full understanding of the kinetics involves an unexpected effect that eludes the chemistry of the reaction, and which is crucially related to the presence of an activation barrier. The resulting analytical description can be exported to real systems, as confirmed by experimental data on epoxy-amine polymerizations, solving a long-standing issue in their mechanistic description

Programmable interactions with biomimetic DNA linkers at fluid membranes and interfaces

At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes where, among other functions, they control cell adhesion, motility and tissue formation. Besides being central to several biological processes, \emph{multivalent interactions} mediated by reactive linkers confined to deformable substrates underpin the design of synthetic-biological platforms and advanced biomimetic materials. Here we review recent advances on the experimental study and theoretical modelling of a heterogeneous class of biomimetic systems in which synthetic linkers mediate multivalent interactions between fluid and deformable colloidal units, including lipid vesicles and emulsion droplets. Linkers are often prepared from synthetic DNA nanostructures, enabling full programmability of the thermodynamic and kinetic properties of their mutual interactions. The coupling of the statistical effects of multivalent interactions with substrate fluidity and deformability gives rise to a rich emerging phenomenology that, in the context of self-assembled soft materials, has been shown to produce exotic phase behaviour, stimuli-responsiveness, and kinetic programmability of the self-assembly process. Applications to (synthetic) biology will also be reviewed.Comment: 63 pages, revie

Replication in Early Evolution

Our understanding of life is essentially shaped by the concept of Darwinian evolution. In fact, the ability to undergo Darwinian evolution is often regarded as a defining property of life. To this end, living or life-like systems must be able to replicate and pass on their genetic material. Replication itself needs to provide for some degree of variability, or mutations, which are selected via their effects on the fitnesses of the replicates. Darwinian evolution is not restricted to vastly complex systems such as organisms or single cells, but also acts on comparatively simple molecular systems. Studying the properties of evolution at this level allows to set boundary conditions on the origins of living systems. In the first part of this thesis, a simple physical environment is studied, where thermal non-equilibrium exerts a selection pressure favouring the replication of longer nucleic acids over short ones. Selection is facilitated against the inherent fitness advantage of shorter molecules, which is due to their smaller size, and thereby overcomes a fundamental problem of early evolution. The environment consists of a submillimetre-sized, elongated cavity with a temperature gradient across. To probe its selection properties, the enzymatic replication of DNA in the polymerase chain reaction (PCR) was used as a model system. PCR is driven by temperature oscillations, which here are provided by the interplay of thermal convection, thermophoresis, and diffusion. Selection arises from an external flux, which alters the convection pattern inside the cavity. A theoretical treatment of the experiments quantitatively models selection and replication characteristics of such thermo-gravitational pores. The laboratory setup mimics porous rock formations in the vicinity of hydrothermal vents at the sea floor, which therefore qualify as a potential scene for early evolution and the origins of life on Earth. The second part presents a reaction network of DNA strands, which replicates sequences of short DNA snippets. Replication of pieces of multiple nucleotides is inspired by the genetic code, where information about amino acids is encoded in trinucleotide codons. The structure of the individual molecules is derived from transfer RNA. Again, replication is driven by thermal oscillations, and proceeds cross-catalytically. It solely relies on base pairing of complementary nucleotide domains, and does not require any ligation chemistry. Therefore, it is detached from the details of the nucleic acids, and would also work with RNA or analogues discussed as potential prebiotic precursors. Considering the replication of individual nucleotides, the replication scheme effectively acts as a proofreading mechanism, improving the fidelity of an upstream polymerization process.Unser Verständnis davon, was Leben ist, wurde wesentlich vom Konzept Darwinscher Evolution geprägt. Tatsächlich wird die Fähigkeit zu Darwinscher Evolution oft als eine definierende Eigenschaft von Leben herangezogen: Ein lebendes oder lebensähnliches System muss in der Lage sein sich zu replizieren und sein genetisches Material zu vererben. Die Replikation muss dabei in gewissem Maße Mutationen zulassen, welche über die Fitness der Nachkommen selektiert werden. Darwinsche Evolution ist nicht auf komplexe Systeme wie Organismen oder Zellen beschränkt, sondern findet auch in einfachen molekularen Systemen statt. Ein Studium auf dieser Ebene erlaubt es außerdem, Randbedingungen an die Entstehung lebender Systeme zu stellen. Im ersten Teil dieser Arbeit wird eine einfache physikalische Umgebung untersucht, in der ein thermisches Nichtgleichgewicht einen Selektionsdruck zugunsten der Replikation von langen Nukleinsäuren vor kürzeren erzeugt. Diese Selektion überwindet den inhärenten Fitness-Vorteil der kürzeren, den diese durch ihre geringere Größe haben, und löst somit ein grundlegendes Problem früher Evolution. Die Umgebung umfasst einen submillimetergroßen, länglichen Hohlraum mit transversalem Temperaturgradienten. Zur Analyse des Selektionsverhaltens wurde die Replikation von DNA mittels Polymerase-Kettenreaktion (PCR) als Modell verwendet. PCR wird von Temperaturoszillationen angetrieben, die hier durch das Zusammenspiel von thermischer Konvektion, Thermophorese und Diffusion hervorgerufen werden. Die Selektion entsteht durch einen äußeren Fluss, der die Konvektion innerhalb des Hohlraums verändert. Eine theoretische Beschreibung der Experimente modelliert das Verhalten solcher thermogravitativen Fallen quantitativ. Der beschriebene Laboraufbau imitiert poröse Felsformationen in der Nähe hydrothermaler Quellen auf dem Meeresgrund, welche somit zu einem potentiellen Schauplatz früher Evolution werden. Der zweite Teil behandelt ein DNA-Reaktionsnetzwerk, welches Abfolgen kurzer DNASequenzen repliziert. Eine solche stückweise Replikation von Oligonukleotiden ist vom genetischen Code inspiriert, in dem Aminosäuren als Trinucleotid-Codons codiert werden. Die Struktur der einzelnen Moleküle des DNA-Netzwerks ist von Transfer-RNA abgeleitet. Die Replikation erfolgt kreuzkatalytisch, wird von Temperaturoszillationen angetrieben und verzichtet auf chemische Ligation. Sie benötigt lediglich die Hybridisierung komplementärer Nukleotiddomänen und würde somit auch mit RNA oder potentiellen RNA-Vorläufern funktionieren. Bezüglich der Replikation einzelner Nukleotide wirkt das Replikationsschema als Korrekturmechanismus eines vorgeschalteten Polymerisationsprozesses

Field-control, phase-transitions, and life's emergence

Instances of critical-like characteristics in living systems at each organizational level as well as the spontaneous emergence of computation (Langton), indicate the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life's origins, brings up a paradox: how could simple organics--lacking the 'soft matter' response properties of today's bio-molecules--have dissipated energy from primordial reactions in a controlled manner for their 'ordering'? Nevertheless, a causal link of life's macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the 'functional-takeover' of a soft magnetic scaffold by organics (c.f. Cairns-Smith's 'crystal-scaffold'). A field-controlled structure offers a mechanism for bootstrapping--bottom-up assembly with top-down control: its super-paramagnetic components obey reversible dynamics, but its dissipation of H-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic network's capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically-oriented system towards a series of phase-transitions with appropriate organic replacements 'taking-over' its functions.Comment: 54 pages, pdf fil

Automated exploration of prebiotic chemical reaction space: progress and perspectives

Prebiotic chemistry often involves the study of complex systems of chemical reactions that form large networks with a large number of diverse species. Such complex systems may have given rise to emergent phenomena that ultimately led to the origin of life on Earth. The environmental conditions and processes involved in this emergence may not be fully recapitulable, making it difficult for experimentalists to study prebiotic systems in laboratory simulations. Computational chemistry offers efficient ways to study such chemical systems and identify the ones most likely to display complex properties associated with life. Here, we review tools and techniques for modelling prebiotic chemical reaction networks and outline possible ways to identify self-replicating features that are central to many origin-of-life models